I have noticed a weird discrepancy between the output of featureCounts when run in paired-end mode vs. single end mode on a paired-end sample.

When comparing the percentage of assigned features I get 45% assigned reads for single-end, which seems to be ok from other posts][1], vs. 5% for paired end mode, the only difference between the two count runs being parameter -p. I have seen a few posts like this one , reporting low assignment rate, and they mostly seem to be on paired end data, answers seem to suggest that something is wrong with the settings or protocol. However, what if that is not the case?